• 2026年
• 2025年
• 2024年

2026年

• Comparison Among Solvent Electrostatic Potentials and a Proposal for Improving the Polarizable Continuum Model
  Y. Kanamaru, N. Yoshida, and T. Matsui
  ACS Omega Article ASAP (2026)
  
• MD–QM/MM Simulation of Amide I Infrared Spectra to Identify Protein Conformational Ensembles: A Case Study of Chignolin
  H.Oshima, S. Fukatsu, W. Sato, K. Yagi and M. Kubo
  Bull. Chem. Soc. Jpn. uoag001 (2026)
  

2025年

• Nature of Adsorption of Amino Acids and Precursors on Interstellar Amorphous Solid Water
  N. Watanabe, Y. Hori, K. Okazawa, Y. Shigeta and M. Shoji
  MNRAS, staf1913 (2025)
  
• Ion Transport Analysis of Anion-Exchange Membranes in Various Hydration States: Combining Experiments with Molecular Dynamics Simulation
  Y. Nara, K. Kasahara, K. Yagi, K. Kim, N. Matubayashi, H. Kawakami, and M. Tanaka
  ACS Appl. Polym. Mater. 7, 13971-13981 (2025)
  
• Toward understanding whole enzymatic reaction cycles using multi-scale molecular simulations
  S. Ito, C. Kobayashi, K. Yagi, and Y. Sugita
  Curr. Op. Struct. Biol. 95, 103153 (2025)
  
• Hyper-Raman Spectra in Solution Based on the Reference Interaction Site Model Self-Consistent Field Method Coupled with the Constrained Spatial Electron Density Distribution and Vibrational Quasi-Degenerate Perturbation Theory
  K. Suda, K. Yagi, and D. Yokogawa
  J. Phys. Chem. Lett. 16, 8666-8672 (2025).
  
• A machine learning approach to designing and understanding tough, degradable polyamides
  Y. Amamoto, C. Koganemaru, K. Kojio, A. Takahara, S. Yamamoto, K. Okazawa, Y. Tsuji, T. Aritake,　and K. Terayama
  npj Comput. Mater. 11, 198 (2025).
  
• Understanding the transition from reversed to conventional conductance decay in single-molecule wires from the effective Hamiltonian and frontier orbital perspective
  K. Okazawa, Y. Tsuji, and K. Yoshizawa
  Bull. Chem. Soc. Jpn. 98, uoaf040 (2025).
  
• 分子性液体の新規拡散方程式理論
  沖田和也
  月刊Precision Medicine 8巻7号 p564-565
  
• Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding protein
  Y. Shinkai, Y. Ding, T. Matsui, G. Devitt, M/ Akiyama, T.-L. Shen, M. Nishida, T. Ida, T. Akaike, S. Mahajan, J. M. Fukuto, Y. Shigeta, Y. Kumagai
  eLife, RP92120 (2025).
  
• High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM
  K. Yagi, K. Gunst, T. Shiozaki, and Y. Sugita
  J. Chem. Theory Comput. 21 4016-4029 (2025).
  
• Fermi resonance in the radiative vibrational cooling dynamics of N2⁢O+
  S. Harayama, S. Kuma, N. Kimura, K. C. Chartkunchand, M. Baba, T. Murakami, T. Takayanagi, K. Yagi, T. Yamaguchi, Y. Nakano and T. Azuma
  Phys. Rev. A, 111, 032803 (2025).
  
• Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning
  Y.-K. Lei, K. Yagi, and Y. Sugita
  J. Chem. Theory Comput. 21, 2695-2711 (2025).
  
• Gold(I)-Catalyzed [2 + 2] and [3 + 2] Cycloadditions of 1,1-Difluoroallenes with Aldehydes: Switchable Syntheses of Fluorinated Oxetanes and Furans
  D. Miyazaki, K. Kudo, Y. Fujiki, N. Watanabe, T. Matsui, J. Ichikawa, and K. Fuchibe
  Org. Lett. 27 3807-3812 (2025).
  

2024年

• 非調和性と環境を考慮した生体分子の振動計算
  八木清, 杉田有治
  生物物理 64, 205-208 (2024).
  
• Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins
  H. Otaki, S. Ishiuchi, M. Fujii, Y. Sugita and K. Yagi
  Phys. Chem. Chem. Phys. 26, 9906-9914 (2024).
  
• Suzuki-Miyaura cross-coupling reaction catalyzed by [R₃Si-IPr]Pd complexes: a computational study
  T. Matsui, J. Fujiwara, N. Fukaya and V. Ya. Lee
  Mendeleev Commun. 34, 1-5 (2024).
  
• Assessment of the Applicability of the LFC/3D-RISM-SCF Scheme for pK_a Prediction in Methanol Solutions
  R. Fujiki, T. Matsui, Y. Shigeta, N. Yoshida, H. Nakano
  Chemistry Letters, 53, upad09 (2024).